The Axis threat to Australia developed gradually and until 1942 was limited to sporadic attacks by German armed merchantmen. The level of Axis naval activity peaked in the first half of 1942 when Japanese submarines conducted anti-shipping patrols off Australia's coast, and Japanese naval aviation attacked several towns in northern Australia. The Japanese submarine offensive against Australia was renewed in the first half of 1943 but was broken off as the Allies pushed the Japanese onto the defensive. Few Axis naval vessels operated in Australian waters in 1944 and 1945, and those that did had only a limited impact.

Due to the episodic nature of the Axis attacks and the relatively small number of ships and submarines committed, Germany and Japan were not successful in disrupting Australian shipping. While the Allies were forced to deploy substantial assets to defend shipping in Australian waters, this did not have a significant impact on the Australian war effort or American-led operations in the South West Pacific Area.

The definition of "Australian waters" used throughout this article is, broadly speaking, the area which was designated the Australia Station prior to the outbreak of war. This vast area consisted of the waters around Australia and eastern New Guinea, and stretching south to Antarctica. From east to west, it stretched from 170° east in the Pacific Ocean to 80° east in the Indian Ocean, and from north to south it stretched from the Equator to the Antarctic. While the eastern half of New Guinea was an Australian colonial possession during the Second World War and fell within the Australia Station, the Japanese operations in these waters formed part of the New Guinea and Solomon Islands Campaigns and were not directed at Australia.

The defence of the Australia Station was the Royal Australian Navy's main concern throughout the war. While RAN ships frequently served outside Australian waters, escort vessels and minesweepers were available to protect shipping in the Australia Station at all times. These escorts were supported by a small number of larger warships, such as cruisers and armed merchant cruisers, for protection against surface raiders. While important military shipping movements were escorted from the start of the war, convoys were not instituted in Australian waters until June 1942. The Australian naval authorities did, however, close ports to shipping at various times following real or suspected sightings of enemy warships or mines prior to June 1942.